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Long's paleontological research has involved field work collecting and studying Palaeozoic fishes throughout Australia,[9] Antarctica,[10] South Africa,[11] Iran,[12] Vietnam,[13] Thailand[14] and China.[15] Long's early research led to the refinement of a new biostratigraphic scheme for dating Palaeozoic sequences in Victoria, Australia. Most of his later research has focussed on collecting and describing the well-preserved 3-dimensional Devonian fishes from the Gogo Formation, Western Australia.[16] His major discoveries from his field expeditions to the Gogo fossil sites (1986–2008) included the first complete skull of an osteolepiform fish, Gogonasus,[17] and a new specimen showing that Gogonasus had large spiracles opening on top of its head.[18] Other discoveries include several new types of dipnoans[19] and arthrodires,[20] and the discovery of the first Devonian fishes showing embryos inside them. This later discovery, published in the journal Nature (May 2008) was the first time that reproduction by internal fertilisation was demonstrated in the extinct Class Placodermi, and the oldest evidence for vertebrate viviparity yet discovered. One of the specimens, named Materpiscis, was also the only known fossil to show a mineralised umbilical structure linked to the unborn embryo. Nature magazine made a short documentary video about this discovery.[21] Other Gogo fish fossils have been found showing remarkable preservation of 3-D muscle tissues, nerve cells and microcapillaries,[22] making this one of the world's most extraordinary sites for exceptional preservation of fossils of this age. One of Long's discoveries, the placoderm Mcnamaraspis,[23] made history by becoming Australia's first official state fossil emblem when it was declared by the Governor as the Western Australian fossil emblem on 5 December 1995.[24]

In addition to his work as a palaeontologist John Long has been prominent as a key science communicator in Australia, mainly through his many popular science books, written for both adults and children, which include works of fiction as well as non-fiction.[25] His book The Rise of Fishes −500 Million Years of Evolution is widely used as a standard reference on fish evolution, and his books dealing with Australian dinosaurs[26] and Mesozoic faunas, and on Australian and New Guinean prehistoric mammals[27] were the first tomes to comprehensively cover these topics. His work collecting fossils in Antarctica was published as a book Mountains of Madness – A Scientist's Odyssey Through Antarctica that gave the first detailed account of a modern scientific expedition to Antarctica as told from the scientist's viewpoint.[28] His work on the international fossil trade, which highlighted problems of fossil smuggling and ignorance of legislation, was made into a 2 part documentary series entitled The Dinosaur Dealers, and published as a book of the same name. He has been active in Australia since the late 1990s dealing with issues of fossil repatriation, legislation and heritage. His books for children include two novels based on cutting edge research that paint vivid pictures of travelling back in time to experience the varied landscapes of prehistoric Australia (Mystery of Devils Roost, Journey to the Dawn of Time)[29][30] as well as non-fiction works dealing mainly with dinosaurs[31] and prehistory, but also with the environment and climate change[32] and the development of human civilizations.[33]

Long's awards include the 2001 Eureka Prize for the Promotion of Science,[34] the 2003 Riversleigh Society Medal for promoting the understanding of Australian prehistory,[35] and the 2008 Australasian Science Prize, a prize awarded across all disciplines of science and medicine each year by Australasian Science magazine for excellence in peer-reviewed research.[36] The 2008 Australasian Science Prize was awarded for the discovery of the world's oldest vertebrate embryos. Long's Literary Awards include the 2006 Best Primary Reference book by the Australian Publishers Association for The Big Picture Book- Life on Earth Unfolding Through Time,[37] which also picked up the 2006 Environmental Award for Children's Literature (non-fiction) and was short-listed for the best information book (Eve Pownall Award of the Children's Book Council) and shortlisted for best children's book in the Western Australian Premiers Literary Awards 2006. In 2007 his book Swimming in Stone-The Amazing Gogo Fossils of the Kimberley was shortlisted for the Science writing prize of the Victorian Premier's Literary Awards.[38] In 2011 John Long and colleagues Kate Trinajstic, Gavin Young & Tim Senden were short-listed for the prestigious Eureka Prize for Scientific Research.[39] In December 2011 John Long received the 2011 Research Medal of the Royal Society of Victoria (Category Earth Sciences).[40]